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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttatgatgacagaagccaatggcattatgcttgctggtgaaagatgattgaagctttgcatttaatcttatttcttttctttttttttcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATACACATTTGGGTGGTGACGACTTTGACAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g03310.t01
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|34543152|gb|CF511384.1|CF511384
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGATGGAGTGTTTGAGGTGCTTTCCACTTCAGGGGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|110360709|gb|EC924030.1|EC924030
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|110376029|gb|EC941068.1|EC941068
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGATGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|56408917|gb|CX017169.1|CX017169
EST:     GGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGACGGAGTGTTCGAGGTGCTTTCCACTTCAGGAGATA
genomic: GGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|161717811|gb|FC065964.1|FC065964
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGATGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|294964596|gb|GW838399.1|GW838399
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|110730008|gb|EE106596.1|EE106596
EST:     GAAACCATTCTGGTATTTGACCTTGGGGGTGAG-ACTTTTGAAGTCTCAN                         TTCCCAAGGTTG
genomic: GAAACCATTCTGGTATTTGACCTTGGGGGTG-GTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTG
EST: gi|161717131|gb|FC065919.1|FC065919
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGATGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
EST: gi|351024502|gb|FQ426311.1|FQ426311
EST:     TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAG                         TTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA
genomic: TGAAACCATTCTGGTATTTGACCTTGGGGGTGGTACTTTTGATGTCTCAGgtaccaagat ... tcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgattgaagctttgcatttaatcttatttcttttctttttttttcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATACACATTTGGGTGGTGACGACTTTGACAAG
                 atttaat  putative branch site (score: 4)
           ctttgcatttaatctt  CT-rich tract
            tttgcatttaatctta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctttatgatgacagaagccaatggcattatgcttgctggtgaaagatgattgaagctttgcatttaatcttatttcttttctttttttttcccctctagTTCTCGAGGTTGGCGACGGAGTGTTTGAGGTGCTTTCCACTTCAGGAGATACACATTTGGGTGGTGACGACTTTGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - tgatgac
- - - - - - - -aagccaa
- - - - - - - - - - - -ggcatta
- - - - - - - - - - - - - - - -gcttgct
- - - - - - - - - - - - - - - - - - - - tgaaaga